ArticleViruses2022
PIMGAVir and Vir-MinION: Two Viral Metagenomic Pipelines for Complete Baseline Analysis of 2nd and 3rd Generation Data.
Article in Viruses, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- ViMOP: a user-friendly and field-applicable pipeline for untargeted viral genome nanopore sequencing.Bioinformatics (Oxford, England) · 2026Article
- Functional genomic analysis ofCurrent research in microbial sciences · 2025Article
- Viral diversity in wild and urban rodents of Yunnan Province, China.Emerging microbes & infections · 2024Article
- Article
- CAPTVRED: an automated pipeline for viral tracking and discovery from capture-based metagenomics samples.Bioinformatics advances · 2024Article
- Virome characterization and identification of a putative parvovirus and poxvirus in bat ectoparasites of Yunnan Province, China.One health (Amsterdam, Netherlands) · 2023Article
- VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing.Bioinformatics (Oxford, England) · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The taxonomic classification of viral sequences is frequently used for the rapid identification of pathogens, which is a key point for when a viral outbreak occurs. Both Oxford Nanopore Technologies (ONT) MinION and the Illumina (NGS) technology provide efficient methods to detect viral pathogens. Despite the availability of many strategies and software, matching them can be a very tedious and time-consuming task. As a result, we developed PIMGAVir and Vir-MinION, two metagenomics pipelines that automatically provide the user with a complete baseline analysis. The PIMGAVir and Vir-MinION pipelines work on 2nd and 3rd generation data, respectively, and provide the user with a taxonomic classification of the reads through three strategies: assembly-based, read-based, and clustering-based. The pipelines supply the scientist with comprehensive results in graphical and textual format for future analyses. Finally, the pipelines equip the user with a stand-alone platform with dedicated and various viral databases, which is a requirement for working in field conditions without internet connection.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.